Matthew E. Ritchie

Restrander improves the orientation and quality control of long-read cDNA data by accurately inferring strandedness and detecting artefacts.

The paper shows that MEK1/2 signaling is essential for male fetal germline development in mice, while FGF signaling has a limited role.

NAb-seq provides a rapid, cost-effective, and species-independent method for sequencing full-length antibody genes from hybridoma cell lines and single B cells, outperforming Sanger sequencing in accuracy and throughput.

The paper benchmarks long-read RNA-sequencing tools using synthetic data to evaluate isoform detection and differential expression analysis performance.

This study shows maternal SMCHD1 is essential for imprinted Xist expression and X chromosome inactivation in mouse embryos and placenta.

The paper develops FLT-seq and FLAMES to characterize full-length isoforms in single cells of human and mouse, identifying thousands of unannotated isoforms and linking them to functional modules and drug resistance mutations.

Glimma 2.0 enhances interactive RNA-seq analysis with reproducible R Markdown integration and improved visualization tools.

This study benchmarks 9 scRNA-seq preprocessing workflows, finding that while they vary in gene detection and quantification, downstream analysis with effective normalization and clustering methods leads to consistent clustering results.

This study analyzes nanopore long-read RNA-seq data using short-read tools to assess differential gene and isoform expression in synthetic and mouse datasets.

NanoMethViz provides an R/Bioconductor package for visualizing long-read methylation data, offering tools to explore methylation patterns at multiple resolutions.

This study identifies Smchd1 as a maternal effect gene that regulates imprinted expression of 16 genes by translating polycomb-mediated histone methylation marks into a heritable chromatin state.

The paper demonstrates that intron reads from RNA-seq are informative and introduces methods to analyze them for transcriptional changes and intron retention.

This study shows that vasoactive intestinal peptide (VIP) regulates ILC3 activity to enhance IL-22 production and confer gut protection through the VIP-VIPR2 pathway.

BiocPkgTools provides a toolkit to access and analyze metadata from the Bioconductor package ecosystem, enabling downstream applications like data mining and graph analytics.

The paper benchmarks scRNA-seq analysis methods using synthetic datasets generated from mixed cancer cell lines, identifying methods that perform well across tasks like normalization, clustering, and integration.

The paper uses long-read nanopore sequencing to detect imprinted DNA methylation and identifies known and novel differentially methylated regions.

SIS-seq links gene expression with cell fate by analyzing clonal progeny, identifying early gene signatures of dendritic cell subset development.

scPipe provides a flexible R/Bioconductor pipeline for preprocessing scRNA-seq data, handling multiple barcoding strategies and generating quality reports for downstream analysis.

Glimma provides interactive graphics for gene expression analysis to enhance data exploration and sharing between bioinformaticians and biologists.

EGSEA combines twelve GSE algorithms to improve gene set enrichment results, outperforming individual methods on simulated and real data.

limma couples gene-wise linear models with empirical Bayes variance moderation and weights; voom extends it to RNA-seq, and added functions test differential splicing and gene sets.